Haplogroup R (Y-DNA)

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Haplogroup R
Possible time of originabout 27,000 years BP[1][2]
Possible place of originpossibly Central Asia[3], South Asia[4], or Siberia[5]
AncestorP1 (P-M45), the only primary clade of P* (P-P295)
DescendantsR1 (R-M173), R2 (R-M479) (R2)
Defining mutationsM207/Page37/UTY2, CTS207/M600/PF5992, CTS2426/M661/PF6033, CTS2913/M667, CTS3229/M672/PF6036/YSC0001265, CTS3622/PF6037, CTS5815/M696, CTS6417/Y480, CTS7876/PF6052, CTS7880/M725/PF6053, CTS8311/M732, CTS9005/M741, CTS10663/M788, CTS11075/M795/P6078, CTS11647/Y369, F33/M603/PF6013, F63/M614/PF6016, F82/M620, F154/M636, F295/M685, F356/M703/PF5919, F370/M708/Y479, F459/Y482, F652/M805, F765, FGC1168, L248.3/M705.3, L747/M702/PF5918/YSC0000287, L760/M642/PF5877/YSC0000286, L1225/M789/YSC0000232, L1347/M792/PF6077/YSC0000233, M613, M628/PF5868, M651/Y296, M718, M734/PF6057/S4/YSC0000201, M760/Y506, M764/PF5953, M799, P224/PF6050, P227, P229/PF6019, P232, P280, P285, PF5938, PF6014/S9 (ISOGG 2016)

Haplogroup R or R-M207, is a Y-chromosome DNA haplogroup. It is both numerous and widespread amongst modern populations.

Some descendant subclades have been found since pre-history in Europe, Central Asia and South Asia. Others have long been present, at lower levels, in parts of West Asia and Africa. Some authorities have also suggested, more controversially, that R-M207 has long been present among Native Americans in North America – a theory that has not yet been widely accepted.

Karafet et al. (2014) and other researchers state that a "rapid diversification ... of K-M526", also known as K2, into K2a and K2b , followed by K2b1 and P (also known as K2b2) "likely occurred in Southeast Asia". This was followed by the relatively rapid "westward expansion" of P1 – the immediate ancestor of both Haplogroups Q and R.[6][7]

Structure[edit]

Human Y-DNA Phylogenetic Tree
Haplogroup R
M207 (R)
M173 (R1)
M420 (R1a)
M459

(R1a1)

(R1a*)

M343 (R1b)
L278

(R1b1)

(R1b*)

M479 (R2)
M124 (R2a)
L263

(R2a1)

F1092

(R2a2)

Y12100

(R2a3)

(R2*)

Origins[edit]

Haplogroup P1 (P-M45), the immediate ancestor of Haplogroup R, likely emerged in Southeast Asia.[6] The SNP M207, which defines Haplogroup R, is believed to have arisen during the Upper Paleolithic era, about 27,000 years ago.[2][1]

Only one confirmed example of basal R* has been found, in 24,000 year old remains, known as MA1, found at Mal'ta–Buret' culture near Lake Baikal in Siberia.[2] (While a living example of R-M207(xM17,M124) was reported in 2012, it was not tested for the SNP M478; the male concerned – among a sample of 158 ethnic Tajik males from Badakshan, Afghanistan – may therefore belong to R2.)

It is possible that neither of the primary branches of R-M207, namely R1 (R-M173) and R2 (R-M479) still exist in their basal, undivergent forms, i.e. R1* and R2*. No confirmed case, either living or dead, has been reported in scientific literature. (Although in the case of R2*, relatively little research has been completed.)

Despite the rarity of R* and R1*, the relatively rapid expansion – geographically and numerically – of subclades from R1 in particular, has often been noted: "both R1a and R1b comprise young, star-like expansions" (Karafet 2008).

The wide geographical distribution of R1b, in particular, has also been noted. Hallast et al. (2014) mentioned that living examples found in Central Asia included:

  • the "deepest subclade" of R-M269 (R1b1a1a2) – the most numerous branch of R1b in Western Europe, and;
  • the rare subclade R-PH155 (R1b1b) found only in one Bhutanese individual and one Tajik.

(While Hallast et al. suggested that R-PH155 was "almost as old as the R1a/R1b split", [8] R-PH155 was later discovered to be a subclade of R-L278 (R1b1) and has been given the phylogenetic name R1b1b.)

Distribution[edit]

Y-haplogroup R-M207 is common throughout Europe, South Asia and Central Asia (Kayser 2003). It also occurs in the Caucasus and Siberia. Some minorities in Africa also carry subclades of R-M207 at high frequencies.

While some indigenous peoples of The Americas and Australasia also feature high levels of R-M207, it is unclear whether these are deep-rooted, or an effect of European colonisation during the early modern era.

R-M207[edit]

Haplogroup R* Y-DNA (xR1,R2) was found in 24,000-year-old remains from Mal'ta in Siberia near Lake Baikal.[5] In 2013, R-M207 was found in one out of 132 males from the Kyrgyz people of East Kyrgyzstan.[9]

R1 (R-M173)[edit]

R-M173, also known as R1, has been common throughout Europe and South Asia since pre-history. It has many branches (Semino 2000 and Rosser 2000).

It is the second most common haplogroup in Indigenous peoples of the Americas following haplogroup Q-M242, especially in the Algonquian peoples of Canada and the United States (Malhi 2008). The reasons for high levels of R-M173 among Native Americans are a matter of controversy:

  • some scholars claim that this is partly or wholly the result of colonial-era immigration from Europe (see e.g. Malhi 2008), whereas;
  • other authorities point to the greater similarity of many R-M173 subclades found in North America to those found in Siberia (e.g. Lell 2002 and Raghavan 2013), suggesting prehistoric immigration from Asia and/or Beringia.

R2 (R-M479)[edit]

Haplogroup R-M479 is defined by the presence of the marker M479. The paragroup for the R-M479 lineage is found predominantly in South Asia, although deep-rooted examples have also been found among Portuguese, Spanish, Tatar (Bashkortostan, Russia), and Ossetian (Caucasus) populations (Myres 2010).

One rare subclade may occur only among Ashkenazi Jews, possibly as a result of a founder effect,

See also[edit]

Genetics[edit]

Y-DNA R-M207 subclades[edit]

Y-DNA backbone tree[edit]

Phylogenetic tree of human Y-chromosome DNA haplogroups [χ 1][χ 2]
"Y-chromosomal Adam"
A00 A0-T [χ 3]
A0 A1 [χ 4]
A1a A1b
A1b1 BT
B CT
DE CF
D E C F
F1  F2  F3  GHIJK
G HIJK
IJK H
IJ K
I   J     LT [χ 5]       K2 [χ 6]
L     T    K2a [χ 7]        K2b [χ 8]     K2c     K2d K2e [χ 9]  
K-M2313 [χ 10]     K2b1 [χ 11] P [χ 12]
NO   S [χ 13]  M [χ 14]    P1     P2
N O Q R

References[edit]

  1. ^ a b ISOGG, Y-DNA Haplogroup R and its Subclades – 2016 (12 December 2016).
  2. ^ a b c Raghavan, M. et al. 2014. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans, Nature, 505, 87–91.
  3. ^ karafet et al 2014.
  4. ^ Hallast2014.
  5. ^ a b Raghavan, Maanasa; Pontus Skoglund; Kelly E. Graf; Mait Metspalu; Anders Albrechtsen; Ida Moltke; Simon Rasmussen; Thomas W. Stafford Jr; Ludovic Orlando; Ene Metspalu; Monika Karmin; Kristiina Tambets; Siiri Rootsi; Reedik Mägi; Paula F. Campos; Elena Balanovska; Oleg Balanovsky; Elza Khusnutdinova; Sergey Litvinov; Ludmila P. Osipova; Sardana A. Fedorova; Mikhail I. Voevoda; Michael DeGiorgio; Thomas Sicheritz-Ponten; Søren Brunak; et al. (2 January 2014). "Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans". Nature. 505 (7481): 87–91. doi:10.1038/nature12736. PMC 4105016. PMID 24256729.
  6. ^ a b Karafet, Tatiana; Mendez, Fernando; Sudoyo, Herawati (2014). "Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia". Nature. 23: 369–373. doi:10.1038/ejhg.2014.106. PMC 4326703. PMID 24896152.
  7. ^ See also: Tumonggor, Karafet et al., 2014, "Isolation, contact and social behavior shaped genetic diversity in West Timor", Journal of Human Genetics Vol. 59, No. 9 (September), pp. 494–503, and; E. Heyer et al., 2013, "Genetic Diversity of Four Filipino Negrito Populations from Luzon: Comparison of Male and Female Effective Population Sizes and Differential Integration of Immigrants into Aeta and Agta Communities", Human Biology, Vol. 85, Iss. 1, p. 201
  8. ^ Hallast, Pille; Batini, Chiara; Zadik, Daniel (2014). "The Y-Chromosome Tree Bursts into Leaf: 13,000 High-Confidence SNPs Covering the Majority of Known Clades". Oxford Journals. 23: 369–73. doi:10.1038/ejhg.2014.106. PMC 4326703. PMID 24896152.
  9. ^ Julie Di Cristofaro , Erwan Pennarun , Stéphane Mazières, Natalie M. Myres, Alice A. Lin, Shah Aga Temori, Mait Metspalu, Ene Metspalu, Michael Witzel, Roy J. King, Peter A. Underhill, Richard Villems & Jacques Chiaroni , 2013, “Afghan Hindu Kush: Where Eurasian Sub-Continent Gene Flows Converge”, ‘’PLoS One’’ (October 18). (17 June 2017.) Figure S7 (XLSX).

Further reading[edit]

External links[edit]

Discussion and projects